VMD-L Mailing List

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Mon Jun 29 2009 - 05:29:33 CDT

On Friday 26 June 2009 14:09:06 Axel Kohlmeyer wrote:
> On Fri, 2009-06-26 at 10:48 +0200, Bjoern Olausson wrote:
> > Hi all,
>
> hi bjoern,
>
> > I am just curious about the analytical capabilities of VMD. So far I used
> > CHARMM to setup, run and analyze my simulations. Now I setup and analyze
> > my simulations with CHARMM but run them with NAMD.
> > There are some deficiencies in the CHARMM programming language which
> > drive me crazy ;) (I am accustomed to the flexible and charming python
> > language)
> >
> > So now my questions might be a bit generic, but is VMD (with TCL in mind)
> > capable of doing all sort of evaluation one can do with CHARMM?
>
> i don't know CHARMM that well, but there is a lot you can do with VMD.
> in total i would expect that VMD is better for doing some operations
> and worse for others. the main difference is that VMD is deliberately
> very agnostic about the data you feed it. on the other hand, missing
> capability can be augmented through customized scripting and writing
> plugins, if you are not afraid of programming.
>
Okay, that sounds promising. Thanks for the clarification.

> > I know this is a very generic question, but I would like to know a bit
> > more before I throw myself into TCL and then realize that I face
> > questions I can't cope with VMD/TCL and see myself creeping back to
> > CHARMM ;-)
>
> the best you can do to inform yourself, is to read through the script
> interface part of the VMD user's guide and have a look at the VMD
> tutorials (and the tcl tutorial bundled with tcl 8.5 or on www.tcl.tk).
>
> as far as the python interface goes, you should keep in mind that this
> is not complete and doesn't have many support packages, but as of the
> latest VMD 1.8.7 beta versions you can call tcl from python (calling
> python from tcl exists a bit longer)
>
Could you redirect me to some VMD 1.8.7 <-> Python tutorial? I would like to
stick to python as much as possible ;-)

> > Ah, one more thing: Can I run VMD/TCL headless on a compute node?
>
> absolutely.
>
Nice, cause its annoying to block the workstation for long running analysis
scripts ;-)

And while I am on it... I am writing a small python script which can combine
multiple output files and selectively plot whatever is plotable ;-)

For this reason I was looking around for the formating of the output file.
Something like that link below for PDB-files:
http://deposit.rcsb.org/adit/docs/pdb_atom_format.html#ATOM

Especially I am interested in the formating and naming of the columns of this
part:

PRESSURE: 29109200 546.983 413.11 92.8291 413.11 -486.118 30.045 92.8291
30.045 -566.529
GPRESSURE: 29109200 388.5 383.831 6.4171 339.175 -407.812 358.594 -111.003
-223.426 -491.163
PRESSAVG: 29109200 32.2755 -27.1969 -120.07 -27.1969 8.01839 -60.9932 -120.07
-60.9932 -3.92224
GPRESSAVG: 29109200 30.6858 -30.7705 -117.957 -14.7335 12.1397 -64.4612
-123.885 -49.5245 -4.49357
ENERGY: 29109200 2828.8126 8444.6120 4596.9095 59.0735
-39328.9221 -1866.4500 0.0000 0.0000 13455.6967
-11810.2678

Thanks for your help

greeting
Bjoern